Insulin resistance is predictive of the development of non-insulin- dependent diabetes mellitus in Pima Indians and this abnormality is associated with decreased rates of glycogen synthesis in skeletal muscle. In vivo-insulin action in Pimas correlates with activities of glycogen synthase (GYS) and of its regulatory enzyme, protein phosphatase type-1 (PP1), and insulin resistant subjects have decreased activities of glycogen-bound PP1, despite an increased mount of immunoreactive PP1 catalytic subunit. Glycogen-associated PP1 activity is determined by an isoform of the catalytic subunit complexed with the glycogen-targeting regulatory (G) subunit, and structural alterations of either component could result in the biochemical abnormalities observed in insulin resistant Pimas. Three genetically distinct PP1 catalytic subunit isoforms are known (PP1 alpha, PP1 beta, and PP1 gamma), and although PP1 beta is believed to be the predominant glycogen-bound form, PP1 alpha, and PP1 gamma may also contribute to the glycogen-associated PP-1 activity. We have determined the exon-intron structure of the genes of PP1 alpha catalytic subunit (PPP1CA; 7 exons), PP1 beta (PPP1CB, 8 exons), PP1 gamma (PPP1CC, 7 exons), and PP1 regulatory G-subunit (PPP1R3, 4 exons) and analyzed PPP1CB first. No sequence alterations were detected by Southern blot analysis or by single-stranded conformational polymorphism (SSCP) of the 8 exons. We have also isolated and analyzed polymorphic CA-repeat markers at PPP1CB, and PPP1CA, and found no evidence for linkage with fasting insulin or insulin action in vivo. We conclude that genetic variations in PPP1CB or PPP1CA are not the cause of PP1 abnormalities or impaired insulin action in Pima Indians. Similar linkage analyses of (CA)-repeat markers at PPP1CC and PPP1R3 are in progress.